chr1-56183430-G-C

Variant names:

• chr1-56183430-G-C
• rs706394
• ENST00000641302.1:n.448+65C>G

Variant summary

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

The ENST00000641302.1(ENSG00000260971):​n.448+65C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0706 in 152,128 control chromosomes in the GnomAD database, including 1,167 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 0.071 (1167 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000260971 ENST00000641302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 1 publications found

Genes affected

ENSG00000260971 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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
ENSG00000260971	ENST00000641302.1	n.448+65C>G		intron_variant	Intron 3 of 4
ENSG00000260971	ENST00000641348.1	n.428+65C>G		intron_variant	Intron 3 of 7
ENSG00000260971	ENST00000641349.1	n.419+65C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0704 AC: 10706 AN: 152010 Hom.: 1164 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.00189

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00591

Gnomad OTH AF: 0.0630

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 12 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 12

African (AFR) AC: 0 AN: 0

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: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0706 AC: 10742 AN: 152128 Hom.: 1167 Cov.: 32 AF XY: 0.0678 AC XY: 5047 AN XY: 74400

African (AFR) AF: 0.229 AC: 9488 AN: 41478

American (AMR) AF: 0.0274 AC: 419 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3466

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5172

South Asian (SAS) AF: 0.0429 AC: 207 AN: 4824

European-Finnish (FIN) AF: 0.00189 AC: 20 AN: 10606

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00591 AC: 402 AN: 67988

Other (OTH) AF: 0.0624 AC: 132 AN: 2116

Alfa AF: 0.0429 Hom.: 94

Bravo AF: 0.0789

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.55
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs706394; hg19: chr1-56649102;