rs7201071

Variant names:

• chr16-51959493-C-T
• rs7201071
• ENST00000736031.1:n.102-2037G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000736031.1(ENSG00000296072):​n.102-2037G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0954 in 152,066 control chromosomes in the GnomAD database, including 1,383 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 0.095 (1383 hom., cov: 31)
• Consequence: ENSG00000296072 ENST00000736031.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 3 publications found

Genes affected

ENSG00000296072 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736031.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296072	ENST00000736031.1		n.102-2037G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0952 AC: 14461 AN: 151950 Hom.: 1375 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0749

Gnomad AMR AF: 0.0835

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.0541

Gnomad SAS AF: 0.0422

Gnomad FIN AF: 0.0278

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0272

Gnomad OTH AF: 0.0955

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

GnomAD4 genome AF: 0.0954 AC: 14501 AN: 152066 Hom.: 1383 Cov.: 31 AF XY: 0.0931 AC XY: 6923 AN XY: 74358

African (AFR) AF: 0.244 AC: 10096 AN: 41424

American (AMR) AF: 0.0843 AC: 1287 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3470

East Asian (EAS) AF: 0.0536 AC: 277 AN: 5168

South Asian (SAS) AF: 0.0424 AC: 204 AN: 4812

European-Finnish (FIN) AF: 0.0278 AC: 295 AN: 10596

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0272 AC: 1853 AN: 68008

Other (OTH) AF: 0.0945 AC: 200 AN: 2116

Alfa AF: 0.0657 Hom.: 307

Bravo AF: 0.107

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.094
DANN	Benign	0.38
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7201071;

hg19: chr16-51993405;