rs10497842

Variant names:

• chr2-199895303-G-A
• rs10497842
• ENST00000413557.7:n.361-640C>T

Variant summary

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

The ENST00000413557.7(ENSG00000232732):​n.361-640C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,104 control chromosomes in the GnomAD database, including 1,741 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 0.14 (1741 hom., cov: 32)
• Consequence: ENSG00000232732 ENST00000413557.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 1 publications found

Genes affected

ENSG00000232732 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927687	XR_241384.6	n.193-640C>T		intron_variant	Intron 2 of 2
LOC101927687	XR_923766.4	n.192+13800C>T		intron_variant	Intron 2 of 3
LOC101927687	XR_923769.4	n.193-12707C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232732	ENST00000413557.7	n.361-640C>T		intron_variant	Intron 2 of 2	3
ENSG00000232732	ENST00000417006.5	n.326-640C>T		intron_variant	Intron 3 of 4	3
ENSG00000232732	ENST00000454153.6	n.158-661C>T		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20945 AN: 151988 Hom.: 1743 Cov.: 32

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.138 AC: 20945 AN: 152104 Hom.: 1741 Cov.: 32 AF XY: 0.132 AC XY: 9838 AN XY: 74356

African (AFR) AF: 0.0963 AC: 3998 AN: 41516

American (AMR) AF: 0.145 AC: 2204 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 683 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.0762 AC: 367 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1310 AN: 10560

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11607 AN: 67990

Other (OTH) AF: 0.178 AC: 376 AN: 2114

Alfa AF: 0.144 Hom.: 218

Bravo AF: 0.142

Asia WGS AF: 0.0400 AC: 141 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.41
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10497842; hg19: chr2-200760026;