9-97592070-TA-TAA

Variant names:

• chr9-97592070-T-TA
• rs11372930
• NM_003275.4:c.1015+637dupA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_003275.4(TMOD1):​c.1015+637dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (18063 hom., cov: 0)
• Consequence: TMOD1 NM_003275.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 1 publications found

Genes affected

TMOD1 (HGNC:11871): (tropomodulin 1) This gene encodes a member of the tropomodulin family. The encoded protein is an actin-capping protein that regulates tropomyosin by binding to its N-terminus, inhibiting depolymerization and elongation of the pointed end of actin filaments and thereby influencing the structure of the erythrocyte membrane skeleton. Multiple transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Oct 2009]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMOD1	NM_003275.4	c.1015+637dupA		intron_variant	Intron 9 of 9	ENST00000259365.9	NP_003266.1
TMOD1	NM_001166116.2	c.1015+637dupA		intron_variant	Intron 9 of 9		NP_001159588.1
TMOD1	XM_047423825.1	c.607+637dupA		intron_variant	Intron 7 of 7		XP_047279781.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMOD1	ENST00000259365.9	c.1015+635_1015+636insA		intron_variant	Intron 9 of 9	1	NM_003275.4	ENSP00000259365.3
TMOD1	ENST00000395211.6	c.1015+635_1015+636insA		intron_variant	Intron 9 of 9	1		ENSP00000378637.2
TMOD1	ENST00000375175.1	c.634+635_634+636insA		intron_variant	Intron 6 of 6	2		ENSP00000364318.1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73135 AN: 151504 Hom.: 18014 Cov.: 0

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.483 AC: 73248 AN: 151620 Hom.: 18063 Cov.: 0 AF XY: 0.481 AC XY: 35649 AN XY: 74066

African (AFR) AF: 0.583 AC: 24058 AN: 41286

American (AMR) AF: 0.495 AC: 7552 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1513 AN: 3468

East Asian (EAS) AF: 0.518 AC: 2668 AN: 5148

South Asian (SAS) AF: 0.392 AC: 1884 AN: 4812

European-Finnish (FIN) AF: 0.426 AC: 4462 AN: 10466

Middle Eastern (MID) AF: 0.545 AC: 157 AN: 288

European-Non Finnish (NFE) AF: 0.435 AC: 29551 AN: 67878

Other (OTH) AF: 0.484 AC: 1021 AN: 2108

Alfa AF: 0.403 Hom.: 997

Asia WGS AF: 0.468 AC: 1627 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.033
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11372930; hg19: chr9-100354352;