rs7771933

chr6-8348673-A-G

Variant summary

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

The ENST00000670476.1(ENSG00000234763):n.229-6025T>C 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 0.346 in 151,932 control chromosomes in the GnomAD database, including 9,986 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 (9986 hom., cov: 31)
• Consequence: ENST00000670476.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670476.1	n.229-6025T>C		intron_variant, non_coding_transcript_variant
	ENST00000651914.1	n.312-6025T>C		intron_variant, non_coding_transcript_variant
	ENST00000655767.1	n.342-6025T>C		intron_variant, non_coding_transcript_variant
	ENST00000661402.1	n.425-6025T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52446 AN: 151816 Hom.: 9971 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.346 AC: 52496 AN: 151932 Hom.: 9986 Cov.: 31 AF XY: 0.337 AC XY: 25037 AN XY: 74268

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.373

Alfa AF: 0.313 Hom.: 1389

Bravo AF: 0.358

Asia WGS AF: 0.254 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.7
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7771933; hg19: chr6-8348906;