rs10249851

Variant names:

• chr7-36021874-A-G
• rs10249851
• ENST00000664385.1:n.119-7737A>G

Variant summary

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

The ENST00000664385.1(ENSG00000232930):​n.119-7737A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.061 in 152,250 control chromosomes in the GnomAD database, including 393 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 0.061 (393 hom., cov: 32)
• Consequence: ENSG00000232930 ENST00000664385.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20
• Publications: 2 publications found

Genes affected

ENSG00000232930 (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 = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375233	NR_187893.1	n.352-7737A>G		intron_variant	Intron 1 of 3
LOC105375233	NR_187894.1	n.98-7737A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232930	ENST00000664385.1	n.119-7737A>G		intron_variant	Intron 1 of 3
ENSG00000232930	ENST00000665884.1	n.386-7737A>G		intron_variant	Intron 1 of 3
ENSG00000287893	ENST00000667088.1	n.68+6233T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0609 AC: 9266 AN: 152132 Hom.: 391 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0610 AC: 9284 AN: 152250 Hom.: 393 Cov.: 32 AF XY: 0.0599 AC XY: 4459 AN XY: 74450

African (AFR) AF: 0.118 AC: 4897 AN: 41528

American (AMR) AF: 0.0433 AC: 662 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4820

European-Finnish (FIN) AF: 0.0308 AC: 327 AN: 10608

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0433 AC: 2946 AN: 68018

Other (OTH) AF: 0.0540 AC: 114 AN: 2112

Alfa AF: 0.0489 Hom.: 366

Bravo AF: 0.0652

Asia WGS AF: 0.0160 AC: 54 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	0.10
DANN	Benign	0.34
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs10249851; hg19: chr7-36061484;