rs4723430

chr7-35508592-G-Achr7-35508592-G-Cchr7-35508592-G-T

Variant summary

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

The ENST00000441150.1(ENSG00000235464):n.30+1642C>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 0.901 in 152,264 control chromosomes in the GnomAD database, including 61,933 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 0.90 (61933 hom., cov: 32)
• Consequence: ENST00000441150.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

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 = 0.949 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
	ENST00000441150.1	n.30+1642C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.901 AC: 137043 AN: 152146 Hom.: 61879 Cov.: 32

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.901 AC: 137156 AN: 152264 Hom.: 61933 Cov.: 32 AF XY: 0.904 AC XY: 67342 AN XY: 74464

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.954

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.884

Alfa AF: 0.879 Hom.: 66607

Bravo AF: 0.899

Asia WGS AF: 0.874 AC: 3039 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	0.30
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4723430; hg19: chr7-35548202;