rs1737049

Positions:

• chr6-29767327-A-G
• chr6-29767327-A-T

Variant summary

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

The variant allele was found at a frequency of 0.352 in 149,046 control chromosomes in the GnomAD database, including 9,520 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 0.35 (9520 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.352 AC: 52434 AN: 148944 Hom.: 9512 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.352 AC: 52465 AN: 149046 Hom.: 9520 Cov.: 32 AF XY: 0.345 AC XY: 25157 AN XY: 72900

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.356

Alfa AF: 0.326 Hom.: 4305

Bravo AF: 0.361

Asia WGS AF: 0.280 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.2
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1737049; hg19: chr6-29735104;