chr7-144044487-A-C

Variant names:

• chr7-144044487-A-C
• rs11976180

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 0.305 in 151,464 control chromosomes in the GnomAD database, including 7,543 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 0.31 (7543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.368 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: 0.305 AC: 46229 AN: 151346 Hom.: 7543 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.00840

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.305 AC: 46237 AN: 151464 Hom.: 7543 Cov.: 32 AF XY: 0.299 AC XY: 22144 AN XY: 74008

African (AFR) AF: 0.373 AC: 15345 AN: 41190

American (AMR) AF: 0.223 AC: 3377 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3466

East Asian (EAS) AF: 0.00841 AC: 43 AN: 5110

South Asian (SAS) AF: 0.283 AC: 1360 AN: 4812

European-Finnish (FIN) AF: 0.254 AC: 2676 AN: 10526

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.317 AC: 21513 AN: 67914

Other (OTH) AF: 0.303 AC: 640 AN: 2112

Alfa AF: 0.297 Hom.: 1897

Bravo AF: 0.304

Asia WGS AF: 0.184 AC: 641 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.67
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs11976180; hg19: chr7-143741580;