chr1-211181496-G-A

Variant names:

• chr1-211181496-G-A
• rs10494934
• ENST00000638880.1:c.-102+661C>T

Variant summary

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

The ENST00000638880.1(ENSG00000283952):​c.-102+661C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0598 in 152,262 control chromosomes in the GnomAD database, including 451 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 0.060 (451 hom., cov: 33)
• Consequence: ENSG00000283952 ENST00000638880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 1 publications found

Genes affected

ENSG00000283952 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 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
ENSG00000283952	ENST00000638880.1	c.-102+661C>T		intron_variant	Intron 3 of 6	5		ENSP00000491750.1
ENSG00000284376	ENST00000450040.2	n.123+661C>T		intron_variant	Intron 3 of 4	5
ENSG00000284376	ENST00000638931.1	n.217+661C>T		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0598 AC: 9099 AN: 152144 Hom.: 447 Cov.: 33

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0650

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0598 AC: 9103 AN: 152262 Hom.: 451 Cov.: 33 AF XY: 0.0627 AC XY: 4669 AN XY: 74436

African (AFR) AF: 0.0143 AC: 594 AN: 41554

American (AMR) AF: 0.0986 AC: 1508 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0531 AC: 184 AN: 3468

East Asian (EAS) AF: 0.185 AC: 959 AN: 5178

South Asian (SAS) AF: 0.160 AC: 770 AN: 4826

European-Finnish (FIN) AF: 0.0436 AC: 462 AN: 10598

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0650 AC: 4423 AN: 68028

Other (OTH) AF: 0.0553 AC: 117 AN: 2114

Alfa AF: 0.0661 Hom.: 241

Bravo AF: 0.0626

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.2
DANN	Benign	0.64
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs10494934; hg19: chr1-211354838;