rs7690819

Positions:

• chr4-111199502-A-G
• chr4-111199502-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000681682.1(ENSG00000288692):​n.616+82230A>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 0.414 in 152,038 control chromosomes in the GnomAD database, including 13,443 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 0.41 (13443 hom., cov: 32)
• Consequence: ENST00000681682.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 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
	ENST00000681682.1	n.616+82230A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62862 AN: 151920 Hom.: 13433 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.414 AC: 62902 AN: 152038 Hom.: 13443 Cov.: 32 AF XY: 0.412 AC XY: 30624 AN XY: 74302

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.382

Alfa AF: 0.445 Hom.: 10265

Bravo AF: 0.401

Asia WGS AF: 0.432 AC: 1498 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	6.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7690819; hg19: chr4-112120658;