rs7749823

Positions:

• chr6-26157851-A-C

Variant summary

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

The ENST00000687674.2(ENSG00000289117):​n.41T>G 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 0.109 in 152,208 control chromosomes in the GnomAD database, including 988 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 0.11 (988 hom., cov: 32)
• Consequence: ENST00000687674.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 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
	ENST00000687674.2	n.41T>G		non_coding_transcript_exon_variant	1/1
	ENST00000707191.1	n.730A>C		non_coding_transcript_exon_variant	1/2
	ENST00000707189.1	n.999+33680A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16562 AN: 152090 Hom.: 991 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.109 AC: 16569 AN: 152208 Hom.: 988 Cov.: 32 AF XY: 0.104 AC XY: 7708 AN XY: 74412

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0953

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.0445

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.118

Alfa AF: 0.121 Hom.: 1135

Bravo AF: 0.115

Asia WGS AF: 0.0520 AC: 180 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7749823; hg19: chr6-26158079; COSMIC: COSV56802692;