7-98815672-T-C

Variant names:

• chr7-98815672-T-C
• rs2894194

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 0.0263 in 128,494 control chromosomes in the GnomAD database, including 131 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 0.026 (131 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0975 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: 0.0263 AC: 3378 AN: 128396 Hom.: 131 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00936

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000701

Gnomad SAS AF: 0.00125

Gnomad FIN AF: 0.000338

Gnomad MID AF: 0.0113

Gnomad NFE AF: 0.000868

Gnomad OTH AF: 0.0217

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

GnomAD4 genome AF: 0.0263 AC: 3385 AN: 128494 Hom.: 131 Cov.: 31 AF XY: 0.0255 AC XY: 1590 AN XY: 62414

African (AFR) AF: 0.100 AC: 3160 AN: 31472

American (AMR) AF: 0.00935 AC: 121 AN: 12944

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3036

East Asian (EAS) AF: 0.000703 AC: 3 AN: 4270

South Asian (SAS) AF: 0.000996 AC: 4 AN: 4018

European-Finnish (FIN) AF: 0.000338 AC: 3 AN: 8886

Middle Eastern (MID) AF: 0.0120 AC: 3 AN: 250

European-Non Finnish (NFE) AF: 0.000868 AC: 53 AN: 61040

Other (OTH) AF: 0.0215 AC: 38 AN: 1768

Alfa AF: 0.0192 Hom.: 0

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.9
DANN	Benign	0.68
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs2894194; hg19: chr7-98413295;