rs1343646

Variant names:

• chr7-97095140-C-A
• rs1343646

Your query was ambiguous. Multiple possible variants found:

• chr7-97095140-C-A
• chr7-97095140-C-G
• chr7-97095140-C-T

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 0.176 in 152,096 control chromosomes in the GnomAD database, including 2,723 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 (2723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 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: 0.176 AC: 26741 AN: 151980 Hom.: 2722 Cov.: 32

Gnomad AFR AF: 0.0874

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.176 AC: 26747 AN: 152096 Hom.: 2723 Cov.: 32 AF XY: 0.174 AC XY: 12958 AN XY: 74350

African (AFR) AF: 0.0875 AC: 3631 AN: 41510

American (AMR) AF: 0.120 AC: 1827 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 876 AN: 3466

East Asian (EAS) AF: 0.147 AC: 762 AN: 5168

South Asian (SAS) AF: 0.168 AC: 811 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2397 AN: 10570

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15697 AN: 67970

Other (OTH) AF: 0.198 AC: 418 AN: 2112

Alfa AF: 0.207 Hom.: 6020

Bravo AF: 0.164

Asia WGS AF: 0.149 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.33
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs1343646; hg19: chr7-96724452;