rs1977772

Positions:

• chr6-140371171-C-G
• chr6-140371171-C-T

Variant summary

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

The ENST00000684511.1(ENSG00000288714):​n.35+56237C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,240 control chromosomes in the GnomAD database, including 2,238 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 0.15 (2238 hom., cov: 33)
• Consequence: ENST00000684511.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

Genes affected

(HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.197 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
	ENST00000684511.1	n.35+56237C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22999 AN: 152122 Hom.: 2241 Cov.: 33

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.151 AC: 22986 AN: 152240 Hom.: 2238 Cov.: 33 AF XY: 0.150 AC XY: 11166 AN XY: 74424

Gnomad4 AFR AF: 0.0370

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0622 Hom.: 89

Bravo AF: 0.149

Asia WGS AF: 0.116 AC: 401 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1977772; hg19: chr6-140692308;