16-81438049-A-G

Variant names:

• chr16-81438049-A-G
• rs310011

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 0.681 in 152,028 control chromosomes in the GnomAD database, including 37,242 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 0.68 (37242 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.905 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: 0.681 AC: 103412 AN: 151908 Hom.: 37186 Cov.: 31

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.681 AC: 103527 AN: 152028 Hom.: 37242 Cov.: 31 AF XY: 0.684 AC XY: 50814 AN XY: 74306

African (AFR) AF: 0.913 AC: 37888 AN: 41498

American (AMR) AF: 0.657 AC: 10044 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1939 AN: 3470

East Asian (EAS) AF: 0.875 AC: 4515 AN: 5158

South Asian (SAS) AF: 0.715 AC: 3450 AN: 4824

European-Finnish (FIN) AF: 0.586 AC: 6188 AN: 10560

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37517 AN: 67930

Other (OTH) AF: 0.663 AC: 1397 AN: 2106

Alfa AF: 0.572 Hom.: 36338

Bravo AF: 0.696

Asia WGS AF: 0.779 AC: 2705 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	1.6
DANN	Benign	0.37
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs310011; hg19: chr16-81471654;