rs1195218

chr7-69159355-G-A

Variant summary

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

The ENST00000661243.1(ENSG00000286466):n.360+3754C>T 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 0.0539 in 152,272 control chromosomes in the GnomAD database, including 269 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 0.054 (269 hom., cov: 32)
• Consequence: ENST00000661243.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0786 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
	ENST00000661243.1	n.360+3754C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0540 AC: 8217 AN: 152154 Hom.: 268 Cov.: 32

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0496

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0804

Gnomad OTH AF: 0.0600

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

GnomAD4 genome AF: 0.0539 AC: 8214 AN: 152272 Hom.: 269 Cov.: 32 AF XY: 0.0523 AC XY: 3892 AN XY: 74444

Gnomad4 AFR AF: 0.0156

Gnomad4 AMR AF: 0.0495

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.0613

Gnomad4 NFE AF: 0.0804

Gnomad4 OTH AF: 0.0589

Alfa AF: 0.0790 Hom.: 490

Bravo AF: 0.0517

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.58
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1195218; hg19: chr7-68624342;