rs524991

Variant names:

• chr1-60864031-G-A
• rs524991
• ENST00000634701.1:n.60+3886C>T

Variant summary

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

The ENST00000663928.1(ENSG00000231252):​n.64+3886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0501 in 152,142 control chromosomes in the GnomAD database, including 259 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 0.050 (259 hom., cov: 32)
• Consequence: ENSG00000231252 ENST00000663928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 4 publications found

Genes affected

ENSG00000231252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0849 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663928.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231252	ENST00000634701.1	TSL:5	n.60+3886C>T		intron	N/A
	ENSG00000231252	ENST00000635290.1	TSL:5	n.82+3886C>T		intron	N/A
	ENSG00000231252	ENST00000663928.1		n.64+3886C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0502 AC: 7628 AN: 152024 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0889

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0297

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.0543

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0501 AC: 7625 AN: 152142 Hom.: 259 Cov.: 32 AF XY: 0.0486 AC XY: 3613 AN XY: 74372

African (AFR) AF: 0.0148 AC: 616 AN: 41510

American (AMR) AF: 0.0889 AC: 1358 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5184

South Asian (SAS) AF: 0.0297 AC: 143 AN: 4812

European-Finnish (FIN) AF: 0.0341 AC: 361 AN: 10574

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0702 AC: 4777 AN: 68002

Other (OTH) AF: 0.0528 AC: 111 AN: 2104

Alfa AF: 0.0471 Hom.: 88

Bravo AF: 0.0547

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.6
DANN	Benign	0.83
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs524991; hg19: chr1-61329703;