chr1-60814879-T-C

Variant names:

• chr1-60814879-T-C
• rs665036
• ENST00000423403.1:n.249+10457A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000423403.1(ENSG00000231252):​n.249+10457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.063 in 152,292 control chromosomes in the GnomAD database, including 398 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 0.063 (398 hom., cov: 32)
• Consequence: ENSG00000231252 ENST00000423403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.45
• Publications: 4 publications found

Genes affected

ENSG00000231252 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101926964	NR_110628.1	n.249+10457A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231252	ENST00000423403.1	n.249+10457A>G		intron_variant	Intron 1 of 5	2
ENSG00000231252	ENST00000634701.1	n.274+10457A>G		intron_variant	Intron 3 of 9	5
ENSG00000231252	ENST00000635290.1	n.296+10457A>G		intron_variant	Intron 3 of 8	5

Frequencies

GnomAD3 genomes AF: 0.0630 AC: 9590 AN: 152174 Hom.: 398 Cov.: 32

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0711

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.0661

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

GnomAD4 genome AF: 0.0630 AC: 9592 AN: 152292 Hom.: 398 Cov.: 32 AF XY: 0.0615 AC XY: 4581 AN XY: 74466

African (AFR) AF: 0.0185 AC: 769 AN: 41566

American (AMR) AF: 0.104 AC: 1597 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0711 AC: 247 AN: 3472

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5184

South Asian (SAS) AF: 0.0313 AC: 151 AN: 4828

European-Finnish (FIN) AF: 0.0516 AC: 548 AN: 10612

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

European-Non Finnish (NFE) AF: 0.0896 AC: 6096 AN: 68014

Other (OTH) AF: 0.0645 AC: 136 AN: 2110

Alfa AF: 0.0817 Hom.: 325

Bravo AF: 0.0666

Asia WGS AF: 0.0220 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	13
DANN	Benign	0.87
PhyloP100		3.5
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs665036; hg19: chr1-61280551;