7-97722311-C-T

Variant names:

• chr7-97722311-C-T
• rs1229439

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 0.279 in 152,116 control chromosomes in the GnomAD database, including 6,359 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 0.28 (6359 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 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: 0.279 AC: 42376 AN: 152000 Hom.: 6355 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0757

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.279 AC: 42394 AN: 152116 Hom.: 6359 Cov.: 32 AF XY: 0.273 AC XY: 20283 AN XY: 74370

African (AFR) AF: 0.234 AC: 9724 AN: 41496

American (AMR) AF: 0.202 AC: 3092 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3472

East Asian (EAS) AF: 0.0758 AC: 393 AN: 5182

South Asian (SAS) AF: 0.209 AC: 1009 AN: 4824

European-Finnish (FIN) AF: 0.303 AC: 3208 AN: 10572

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23295 AN: 67970

Other (OTH) AF: 0.238 AC: 502 AN: 2108

Alfa AF: 0.317 Hom.: 30160

Bravo AF: 0.269

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.50
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1229439; hg19: chr7-97351623;