chr8-6885036-G-A

Variant names:

• chr8-6885036-G-A
• rs2738169
• ENST00000531701.2:n.602-86G>A

Variant summary

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

The ENST00000531701.2(GS1-24F4.2):​n.602-86G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,158 control chromosomes in the GnomAD database, including 3,493 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 0.21 (3493 hom., cov: 32)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• Publications: 5 publications found

Genes affected

GS1-24F4.2 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.2	n.602-86G>A		intron_variant	Intron 4 of 4	3
GS1-24F4.2	ENST00000772759.1	n.352-86G>A		intron_variant	Intron 2 of 2
GS1-24F4.2	ENST00000772760.1	n.794-86G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31374 AN: 152018 Hom.: 3486 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.200 AC: 4 AN: 20 Hom.: 0 AF XY: 0.167 AC XY: 3 AN XY: 18

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.167 AC: 1 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 2 AN: 8

Other (OTH) AF: 0.250 AC: 1 AN: 4

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.010549), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.206 AC: 31389 AN: 152138 Hom.: 3493 Cov.: 32 AF XY: 0.214 AC XY: 15896 AN XY: 74372

African (AFR) AF: 0.195 AC: 8101 AN: 41492

American (AMR) AF: 0.218 AC: 3329 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3472

East Asian (EAS) AF: 0.387 AC: 2002 AN: 5176

South Asian (SAS) AF: 0.234 AC: 1127 AN: 4822

European-Finnish (FIN) AF: 0.330 AC: 3485 AN: 10574

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12351 AN: 67998

Other (OTH) AF: 0.179 AC: 377 AN: 2112

Alfa AF: 0.185 Hom.: 11711

Bravo AF: 0.198

Asia WGS AF: 0.262 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.19
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2738169; hg19: chr8-6742558;