rs324654

chr7-137022995-T-C

Variant summary

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

The NR_046103.1(LOC349160):n.341+9799A>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 0.944 in 152,066 control chromosomes in the GnomAD database, including 67,919 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 0.94 (67919 hom., cov: 33)
• Consequence: LOC349160 NR_046103.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC349160	NR_046103.1	n.341+9799A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000586239.5	n.273+9799A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143387 AN: 151948 Hom.: 67865 Cov.: 33

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.944 AC: 143497 AN: 152066 Hom.: 67919 Cov.: 33 AF XY: 0.942 AC XY: 70048 AN XY: 74330

Gnomad4 AFR AF: 0.987

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.967

Gnomad4 NFE AF: 0.938

Gnomad4 OTH AF: 0.939

Alfa AF: 0.940 Hom.: 62784

Bravo AF: 0.943

Asia WGS AF: 0.826 AC: 2871 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs324654; hg19: chr7-136707742;