16-56663179-G-T

Variant names:

• chr16-56663179-G-T
• rs7194895
• XR_001752208.2:n.601G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001752208.2(LOC101927536):​n.601G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,004 control chromosomes in the GnomAD database, including 9,027 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 0.34 (9027 hom., cov: 32)
• Consequence: LOC101927536 XR_001752208.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

Genes affected

LOC101927536 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927536	XR_001752208.2	n.601G>T		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51733 AN: 151884 Hom.: 9015 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.341 AC: 51770 AN: 152004 Hom.: 9027 Cov.: 32 AF XY: 0.343 AC XY: 25469 AN XY: 74316

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.326

Alfa AF: 0.321 Hom.: 3466

Bravo AF: 0.339

Asia WGS AF: 0.313 AC: 1091 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	1.8
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7194895; hg19: chr16-56697091; COSMIC: COSV57622462;