7-87499549-T-C

Variant names:

• chr7-87499549-T-C
• rs6946119

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 0.18 in 151,970 control chromosomes in the GnomAD database, including 3,117 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 0.18 (3117 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 21 publications found

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 (AMR) allele frequency at 95% confidence interval = 0.245 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: 0.180 AC: 27331 AN: 151852 Hom.: 3113 Cov.: 31

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.180 AC: 27333 AN: 151970 Hom.: 3117 Cov.: 31 AF XY: 0.179 AC XY: 13262 AN XY: 74262

African (AFR) AF: 0.0496 AC: 2059 AN: 41476

American (AMR) AF: 0.252 AC: 3841 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1190 AN: 3462

East Asian (EAS) AF: 0.131 AC: 676 AN: 5162

South Asian (SAS) AF: 0.198 AC: 954 AN: 4810

European-Finnish (FIN) AF: 0.147 AC: 1555 AN: 10544

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16346 AN: 67948

Other (OTH) AF: 0.227 AC: 478 AN: 2108

Alfa AF: 0.223 Hom.: 14507

Bravo AF: 0.180

Asia WGS AF: 0.160 AC: 556 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	2.9
DANN	Benign	0.77
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs6946119; hg19: chr7-87128865;