rs7077606

Variant names:

• chr10-53647331-C-T
• rs7077606

Variant summary

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

The variant allele was found at a frequency of 0.153 in 151,828 control chromosomes in the GnomAD database, including 1,969 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 0.15 (1969 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 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

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23256 AN: 151712 Hom.: 1969 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0959

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.153 AC: 23252 AN: 151828 Hom.: 1969 Cov.: 31 AF XY: 0.155 AC XY: 11502 AN XY: 74208

African (AFR) AF: 0.114 AC: 4708 AN: 41358

American (AMR) AF: 0.147 AC: 2242 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0959 AC: 332 AN: 3462

East Asian (EAS) AF: 0.137 AC: 704 AN: 5144

South Asian (SAS) AF: 0.301 AC: 1449 AN: 4816

European-Finnish (FIN) AF: 0.159 AC: 1669 AN: 10526

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11496 AN: 67958

Other (OTH) AF: 0.164 AC: 345 AN: 2108

Alfa AF: 0.144 Hom.: 190

Bravo AF: 0.146

Asia WGS AF: 0.221 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.34
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7077606; hg19: chr10-55407091; COSMIC: COSV68817864;