rs7178130

Variant names:

• chr15-72685861-G-A
• rs7178130
• NM_001350932.3:c.-236C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-72685861-G-A
• chr15-72685861-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350932.3(HIGD2B):​c.-236C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 371,740 control chromosomes in the GnomAD database, including 62,861 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.53 (22979 hom., cov: 32)
  • Exomes 𝑓: 0.59 (39882 hom.)
• Consequence: HIGD2B NM_001350932.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 17 publications found

Genes affected

HIGD2B (HGNC:26984): (HIG1 hypoxia inducible domain family member 2B) Predicted to be involved in mitochondrial respirasome assembly. Predicted to be integral component of membrane. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HIGD2B	NM_001350932.3	c.-236C>T		5_prime_UTR_variant	Exon 1 of 3	ENST00000311755.6	NP_001337861.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HIGD2B	ENST00000311755.6	c.-236C>T		5_prime_UTR_variant	Exon 1 of 3	1	NM_001350932.3	ENSP00000307951.3

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80068 AN: 151924 Hom.: 22998 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.554

GnomAD4 exome AF: 0.587 AC: 129055 AN: 219696 Hom.: 39882 Cov.: 0 AF XY: 0.589 AC XY: 68419 AN XY: 116118

African (AFR) AF: 0.323 AC: 2337 AN: 7240

American (AMR) AF: 0.503 AC: 4719 AN: 9374

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 4245 AN: 6332

East Asian (EAS) AF: 0.208 AC: 2505 AN: 12064

South Asian (SAS) AF: 0.591 AC: 18878 AN: 31960

European-Finnish (FIN) AF: 0.652 AC: 7587 AN: 11630

Middle Eastern (MID) AF: 0.655 AC: 584 AN: 892

European-Non Finnish (NFE) AF: 0.634 AC: 81079 AN: 127962

Other (OTH) AF: 0.582 AC: 7121 AN: 12242

GnomAD4 genome AF: 0.527 AC: 80063 AN: 152044 Hom.: 22979 Cov.: 32 AF XY: 0.530 AC XY: 39366 AN XY: 74328

African (AFR) AF: 0.325 AC: 13475 AN: 41400

American (AMR) AF: 0.529 AC: 8087 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2334 AN: 3472

East Asian (EAS) AF: 0.225 AC: 1164 AN: 5178

South Asian (SAS) AF: 0.577 AC: 2784 AN: 4822

European-Finnish (FIN) AF: 0.655 AC: 6927 AN: 10582

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43302 AN: 67988

Other (OTH) AF: 0.548 AC: 1157 AN: 2110

Alfa AF: 0.580 Hom.: 39215

Bravo AF: 0.508

Asia WGS AF: 0.384 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.8
DANN	Benign	0.85
PhyloP100		-0.23
PromoterAI		-0.034	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7178130; hg19: chr15-72978202; COSMIC: COSV51440585; COSMIC: COSV51440585;